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- PDB-1re9: CRYSTAL STRUCTURE OF CYTOCHROME P450-CAM WITH A FLUORESCENT PROBE... -

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Basic information

Entry
Database: PDB / ID: 1re9
TitleCRYSTAL STRUCTURE OF CYTOCHROME P450-CAM WITH A FLUORESCENT PROBE D-8-AD (ADAMANTANE-1-CARBOXYLIC ACID-5-DIMETHYLAMINO-NAPHTHALENE-1-SULFONYLAMINO-OCTYL-AMIDE)
ComponentsCytochrome P450-cam
KeywordsOXIDOREDUCTASE / Monooxygenase / Conformational States / Substrate-linked Sensitizers / SUBSTRATE-BINDING / DANSYL / ADAMANTANE / ADAMANTANE-1-CARBOXYLIC ACID / 4-(5-DIMETHYLAMINO-NAPHTHALENE-1-SULFONYLAMINO)-OCTYL]-AMIDE / CHANNEL
Function / homology
Function and homology information


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DSO / PROTOPORPHYRIN IX CONTAINING FE / : / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsHays, A.-M.A. / Dunn, A.R. / Gray, H.B. / Stout, C.D. / Goodin, D.B.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Conformational states of cytochrome P450cam revealed by trapping of synthetic molecular wires.
Authors: Hays, A.M. / Dunn, A.R. / Chiu, R. / Gray, H.B. / Stout, C.D. / Goodin, D.B.
History
DepositionNov 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450-cam
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9707
Polymers46,5891
Non-polymers1,3826
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.565, 75.941, 92.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450-cam / Camphor 5-monooxygenase / P450cam


Mass: 46588.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: CAMC, CYP101 / Plasmid: PUS200 / Production host: Escherichia coli (E. coli) / Strain (production host): TBY / References: UniProt: P00183, camphor 5-monooxygenase

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Non-polymers , 5 types, 279 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-DSO / ADAMANTANE-1-CARBOXYLIC ACID-5-DIMETHYLAMINO-NAPHTHALENE-1-SULFONYLAMINO-OCTYL-AMIDE


Mass: 539.772 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H45N3O3S
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: CITRATE, PEG, KCL, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 27, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→8 Å / Num. obs: 76782 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.97 % / Biso Wilson estimate: 12.6 Å2 / Rsym value: 0.077 / Net I/σ(I): 12.4
Reflection shellResolution: 1.45→1.51 Å / Mean I/σ(I) obs: 1.3 / Rsym value: 0.43 / % possible all: 90

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
CNSrefinement
SHELXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CPP

2cpp


Resolution: 1.45→8 Å / Num. parameters: 32124 / Num. restraintsaints: 40016 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56.
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 3822 -RANDOM
Rwork0.1598 ---
all0.1621 76782 --
obs0.1621 76782 90.6 %-
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 3149 / Occupancy sum non hydrogen: 3573
Refinement stepCycle: LAST / Resolution: 1.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3237 0 94 273 3604
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0267
X-RAY DIFFRACTIONs_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.062
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.03
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps0.088

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